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- PDB-6rvm: Cell division protein FtsZ from Staphylococcus aureus, apo form -

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Basic information

Entry
Database: PDB / ID: 6rvm
TitleCell division protein FtsZ from Staphylococcus aureus, apo form
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.155 Å
AuthorsFernandez-Tornero, C. / Andreu, J.M. / Canosa-Valls, A.J.
CitationJournal: Febs J. / Year: 2020
Title: Nucleotide-induced folding of cell division protein FtsZ from Staphylococcus aureus.
Authors: Huecas, S. / Canosa-Valls, A.J. / Araujo-Bazan, L. / Ruiz, F.M. / Laurents, D.V. / Fernandez-Tornero, C. / Andreu, J.M.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
D: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,83725
Polymers127,5324
Non-polymers1,30521
Water1,35175
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3628
Polymers31,8831
Non-polymers4797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9752
Polymers31,8831
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2988
Polymers31,8831
Non-polymers4157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2027
Polymers31,8831
Non-polymers3196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.564, 78.805, 225.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cell division protein FtsZ


Mass: 31883.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A031

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Non-polymers , 5 types, 96 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.1 M (NH4)2SO4, 0.1 M MES pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 70836 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 2.15→2.27 Å / Num. unique obs: 10226 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGJ

3wgj


Resolution: 2.155→39.161 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.2558 3524 4.99 %
Rwork0.2295 --
obs0.2308 70658 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.155→39.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8575 0 67 75 8717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028674
X-RAY DIFFRACTIONf_angle_d0.45411697
X-RAY DIFFRACTIONf_dihedral_angle_d14.2125269
X-RAY DIFFRACTIONf_chiral_restr0.0451417
X-RAY DIFFRACTIONf_plane_restr0.0031545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1545-2.1840.32881410.32552657X-RAY DIFFRACTION100
2.184-2.21520.35341360.31432634X-RAY DIFFRACTION100
2.2152-2.24830.29861410.31122664X-RAY DIFFRACTION100
2.2483-2.28340.35091540.30332623X-RAY DIFFRACTION100
2.2834-2.32080.32041280.29422667X-RAY DIFFRACTION100
2.3208-2.36080.3411450.28442632X-RAY DIFFRACTION100
2.3608-2.40380.341230.28032694X-RAY DIFFRACTION100
2.4038-2.450.2741290.27012672X-RAY DIFFRACTION100
2.45-2.50.32951350.28152675X-RAY DIFFRACTION100
2.5-2.55440.34761420.27222653X-RAY DIFFRACTION100
2.5544-2.61380.30451540.26622662X-RAY DIFFRACTION100
2.6138-2.67910.3181440.27422645X-RAY DIFFRACTION100
2.6791-2.75150.3331370.28552661X-RAY DIFFRACTION100
2.7515-2.83250.33831360.27562670X-RAY DIFFRACTION100
2.8325-2.92390.29581520.28142668X-RAY DIFFRACTION100
2.9239-3.02830.30611490.26572677X-RAY DIFFRACTION100
3.0283-3.14950.28941200.2742713X-RAY DIFFRACTION100
3.1495-3.29280.28671370.27492679X-RAY DIFFRACTION100
3.2928-3.46630.29661390.23992688X-RAY DIFFRACTION100
3.4663-3.68330.28661320.22522715X-RAY DIFFRACTION100
3.6833-3.96750.21071410.20872708X-RAY DIFFRACTION100
3.9675-4.36630.24141560.19772706X-RAY DIFFRACTION100
4.3663-4.9970.22561400.17922739X-RAY DIFFRACTION100
4.997-6.29140.2191530.22152758X-RAY DIFFRACTION99
6.2914-39.16770.20061600.19822874X-RAY DIFFRACTION99

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